Domain shuffling

It is now apparent that many bacterial cellulases are composed of two or more structural and functional units or domains and it has been suggested that such enzymes arose by a process of domain shuffling (1). The domains may be catalytic or non-catalytic and their occurrence is often indicated in the primary protein structure by an intervening... 

In an effort to formulate novel approaches to complex library synthesis, Porco and coworkers have prepared a hybrid oxime library (10) via chemical domain shuffling . In this approach, discrete fragments or chemical domains may be shuffled to prepare complex hybrid structures (Scheme 9). 

The T. reesei enzymes could also be cleaved into separate domains by proteolysis, and this was discussed elsewhere (Claeyssens, M., and Tomme, P., this volume). Suffice it to emphasize here that the genes encoding cellulases in C. fimi and T. reesei appear to have arisen by domain shuffling and that the enzymes they encode appear to interact with cellulose in a comparable manner, i.e., a catalytic domain is held on the substrate by a binding domain. Cellulases from the bacterium Clostridium thermocellum also contained sequences analogous to Pro-Thr boxes as well as highly conserved carboxyl terminal sequences (2,17,18). It remains to be seen if they have functional organizations similar to those of the C. fimi and T. reesei enzymes. 

A. The VOC Superfamily Reengineering the Scaffold through Wholesale Domain Shuffling... 

Hurt JA, Thibodeau SA, Hirsh AS, Pabo CO, Joung JK (2003) Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc Natl Acad Sci USA 100 12271-12276... 

Evidence for domain recruitment has been identified in a wide variety of proteins [47], mechanistically ranging from simple N- or C-terminal fusion to multiple internal insertions and possibly circular permutations [48]. A recent analysis of proteins in the protein structure database (PDB) has further indicated that structural rearrangements as a result of domain shuffling have significantly contributed to today s functional diversity [49]. A brief overview of the various modes of domain recruitment and their effects on function, is presented on examples of /lex-barrel structures. 

Domains with identical or similar biochemical activities do not necessarily have the same fold. Conversely domains with different biochemical activities may group within the same fold. Recognition of some distant evolutionary events (such as unequal recombination, circular permutation and domain shuffling) has gradually made it possible to describe the basic complement of protein domains that was present in the last common ancestor (Aravind et al, 2002). 

However, one disadvantage of this domain shuffling method is that many resulting hybrid PKSs are unproductive. An uittesolved problem in this field is the limited insight into the structure and mode of action of the PKS. Schulz et al. presented the first example of using site-directed... 

For leukocytes, it has recently been estimated that around one third of all cell surface proteins contain at least one Ig domain [2]. The evolutionary success of the Ig fold is likely to be due to a combination of factors such as its resistance to extracellular proteases and the fact that Ig domains are usually encoded by exons with phase 1 splice junctions close to the domain boundary that are permissive to exon duplication and domain shuffling. Such processes would be fundamental in allowing the generation and selection of the wide variety of IgSF molecules that are now known to exist [2]. 

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